Microbial bioremediation of persistent organic pollutants (POP)

Group 6: Javier López, Pablo Sánchez-Izquierdo, Víctor Fiérrez and Laura Casanovas

What is bioremediation?

OUR DATA

POP (persistent organic pollutants): clean-up technique for reclaiming POP-contaminated environments. It is attractive, eco-friendly and cost-efficient.

Manually curated integrative database dedicated to microbial bioremediation of persistent organic pollutants (POP) research.

  • Genes
  • Strains
  • Sequences (Complementary)
  • Compound
  • Calculated properties 01

We added the corresponding sequence to each sample.

Final dataset size: 5733 observations of 12 variables

GOAL

Elucidate patterns within organisms with bioremediation potential. To promote more effective and sustainable solutions.

CLEANING

  • Select columns of interest: Compound Name, Enzyme Name, Encoding Gene, KEGG Orthology, Organism, GenBankID, Strain ID/Microorganism, UniProt ID, Protein ID, Continent, Country, Isolation source, Habitat notes
  • Deal with null values
    • Delete columns with majority null values (except from KEGG Orthology)
  • Change variable names
  • Standarization of naming convention of: Encoding Gene, Continent, Country

DATA EXPLORATION: ORGANISM DISTRIBUTION

We will do our study only with Bacteria samples.

DATA EXPLORATION: GENES VS COMPOUNDS

  • Too many genes, is there anyting we can do?
    • USE: KEGG Orthology

RESULTS: World Distribution of bioremediation

RESULTS: Orthology Analysis

RESULTS: Sequence Analysis

For each compound:

  • MSA
  • Phylogenetic tree
  • Core sequence
  • Sequence logo

CONCLUSIONS

  1. Bioremediation organisms studied up to date are mainly Bacteria
  1. There are still a lot of countries to be explored
  1. Chlorocyclohexane and chlorobenzene degradation pathway is involved in the bioremediation of many POP compounds
  1. Core sequence LOGO for genes degrading the same compounds have been determined by multiple sequence alignment
  1. Core sequence LOGO are very different depending on what compound they target and they can be grouped by proximity by performing a phylogenetic tree analysis

THANK YOU! Microbial bioremediation of persistent organic pollutants (POP)

G6: Javier López, Pablo Sánchez-Izquierdo, Víctor Fiérrez and Laura Casanovas